[English] 日本語
Yorodumi- PDB-5j7n: Crystal structure of a small heat-shock protein from Xylella fast... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j7n | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high order structure | ||||||
Components | Low molecular weight heat shock protein | ||||||
Keywords | CHAPERONE / Small heat shock protein / Xylella fastidiosa / alpha-crystallin domain / citrus variegated chlorosis | ||||||
Function / homology | Function and homology information : / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Xylella fastidiosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Fonseca, E.M.B. / Scorsato, V. / dos Santos, C.A. / Tomazini Jr., A. / Aparicio, R. / Polikarpov, I. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure. Authors: Fonseca, E.M. / Scorsato, V. / Dos Santos, M.L. / Junior, A.T. / Tada, S.F. / Dos Santos, C.A. / de Toledo, M.A. / de Souza, A.P. / Polikarpov, I. / Aparicio, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5j7n.cif.gz | 58 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5j7n.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 5j7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/5j7n ftp://data.pdbj.org/pub/pdb/validation_reports/j7/5j7n | HTTPS FTP |
---|
-Related structure data
Related structure data | 3glaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17880.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xylella fastidiosa (strain 9a5c) (bacteria) Strain: 9a5c / Gene: XF_2234 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PBB0 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES sodium salt pH 7.5, 0.3 M sodium citrate, 20% 2-propanol, 15% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→68.94 Å / Num. obs: 4089 / % possible obs: 98 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 3.5 / % possible all: 97.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GLA Resolution: 2.9→40.452 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.33 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→40.452 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|